Related papers: Kink solitons in DNA
We present a study of the bend angle distribution of semiflexible polymers of short and intermediate lengths within the wormlike chain model. This enables us to calculate the elastic response of a stiff molecule to a bending moment. Our…
An impact of kink-type solitons on infrared lattice vibrations is studied for incommensurate Frenkel-Kontorova model. It is shown that the vibration of particles involved into the kink formation is very similar to that in a gap mode around…
Kink defects in the 90-degree partial dislocation in silicon are studied using a linear-scaling density-matrix technique. The asymmetric core reconstruction plays a crucial role, generating at least four distinct kink species as well as…
We investigate the dynamical behavior of simple modules composed of two genes with two or three regulating connections. Continuous dynamics for mRNA and protein concentrations is compared to a Boolean model for gene activity. Using a…
We study the effect of transcription on the kinetics of DNA supercoiling in 3D by means of Brownian dynamics simulations of a single nucleotide resolution coarse-grained model for double stranded DNA. By accounting for the action of a…
The aim of this work is to establish a linear instability result of stationary, kink and kink/anti-kink soliton profile solutions for the sine-Gordon equation on a metric graph with a structure represented by a $\mathcal Y$-junction. The…
Complex DNA topological structures, including polymer loops, are frequently observed in biological processes when protein molecules simultaneously bind to several distant sites on DNA. However, the molecular mechanisms of formation of these…
We investigate the sequence-dependent behaviour of localised excitations in a toy, nonlinear model of DNA base-pair opening originally proposed by Salerno. Specifically we ask whether ``breather'' solitons could play a role in the…
This paper presents a molecular mechanics study for new nanorobotic structures using molecular dynamics (MD) simulations coupled to virtual reality (VR) techniques. The operator can design and characterize through molecular dynamics…
We study the dynamical behaviour of the proton transfer in the hydrogen bonds in the base-pairs of the double helices of the DNA type. Under the assumption that the elastic and the tunnelling degrees of freedom may be coupled, we derive a…
DNA and other biopolymers differ from classical polymers due to their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the `torsional…
Capturing the physical organisation and dynamics of genomic regions is one of the major open challenges in biology. The kinetoplast DNA (kDNA) is a topologically complex genome, made by thousands of DNA (mini and maxi) circles interlinked…
The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single…
A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of…
We study discrete solitons (kinks) accessible in state-of-the-art trapped ion experiments, considering zigzag crystals and quasi-3D configurations, both theoretically and experimentally. We first extend the theoretical understanding of…
Helical molecules change their twist number under the effect of a mechanical load. We study the twist-stretch relation for a set of short DNA molecules modeled by a mesoscopic Hamiltonian. Finite temperature path integral techniques are…
We present a new dynamical model of DNA. This model has two degrees of freedom per base-pair: one radial variable related to the opening of the hydrogen bonds and an angular one related to the twisting of each base-pair responsible for the…
By resorting to a model inspired to the standard Davydov and Holstein-Fr\"ohlich models, in the present paper we study the motion of an electron along a chain of heavy particles modelling a sequence of nucleotides proper to a DNA fragment.…
The continuum-rod model has emerged as an efficient tool to describe the long-length-scale structural-deformations of DNA which are critical to understanding the nature of many biological processes such as gene expression. However, a…
It is a standard exercise in mechanical engineering to infer the external forces and torques on a body from its static shape and known elastic properties. Here we apply this kind of analysis to distorted double-helical DNA in complexes with…